Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013537133.1 THEAM_RS01925 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_000185805.1:WP_013537133.1 Length = 406 Score = 474 bits (1220), Expect = e-138 Identities = 244/404 (60%), Positives = 316/404 (78%), Gaps = 1/404 (0%) Query: 1 MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60 MALIVQKFGGTS+GSIERI VA++V + +E G+ +VVV+SAM+GET+RLI+L K IT + Sbjct: 1 MALIVQKFGGTSMGSIERIRLVAQRVLEEKEKGNQVVVVVSAMAGETDRLIELVKSITPE 60 Query: 61 PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120 P R++D +VSTGEQV+ LL++ L G PAV+ +G Q I TD + KARI+ ID ++ Sbjct: 61 PNERDMDFVVSTGEQVSAGLLSITLNHLGHPAVALSGWQAGIKTDDAFTKARIISIDTER 120 Query: 121 IRADLKEGRVVVVAGFQGVDEHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 I LKEG++VV+ GFQG+ E G ITTLGRGGSDT+ VALAAAL AD C IYTDVDGVYT Sbjct: 121 ILKHLKEGKIVVITGFQGITEEGEITTLGRGGSDTSAVALAAALNADRCDIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKEGPGTLI 240 DPR+VP+AR++ +++EEMLE+ASLG+KVLQIRSVEFA KY VPLRV +F+ GTLI Sbjct: 181 ADPRIVPEARKIPVLSYEEMLELASLGAKVLQIRSVEFAMKYKVPLRVRSTFQPDEGTLI 240 Query: 241 TIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIVQNVAH 300 +E+E+ME+ ++ GIA N++EA++T+ VPD PG+A K+ ++ +NI VDMIVQNV+ Sbjct: 241 K-EEDETMERVVVRGIAHNKNEARITVVRVPDKPGIAAKLFDALAEANIPVDMIVQNVSV 299 Query: 301 DNTTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHAGVASCM 360 D TD +FTV +N+ +KA+ + + A+EIGAREVI D KIAKVSIVG+GMRSHAGVA + Sbjct: 300 DGYTDISFTVDKNDAQKAEKITQKVAQEIGAREVIRDDKIAKVSIVGLGMRSHAGVAGKV 359 Query: 361 FEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404 FE LA INI MISTSEIK+S +++EK+ ELAVR LH AF LD Sbjct: 360 FETLANYGINILMISTSEIKISCIIDEKFTELAVRVLHEAFGLD 403 Lambda K H 0.316 0.133 0.358 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 482 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 411 Length of database: 406 Length adjustment: 31 Effective length of query: 380 Effective length of database: 375 Effective search space: 142500 Effective search space used: 142500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_013537133.1 THEAM_RS01925 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (EC 2.7.2.4))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00656.hmm # target sequence database: /tmp/gapView.28371.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00656 [M=407] Accession: TIGR00656 Description: asp_kin_monofn: aspartate kinase, monofunctional class Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-153 496.1 11.2 4.7e-153 495.9 11.2 1.0 1 lcl|NCBI__GCF_000185805.1:WP_013537133.1 THEAM_RS01925 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185805.1:WP_013537133.1 THEAM_RS01925 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 495.9 11.2 4.7e-153 4.7e-153 1 405 [. 1 401 [. 1 403 [. 0.98 Alignments for each domain: == domain 1 score: 495.9 bits; conditional E-value: 4.7e-153 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisp 69 + liVqKFGGts+gs+eri+ +a++vl+e+++g++vvVVvSAm+++td+l+el+ ++i e+++ lcl|NCBI__GCF_000185805.1:WP_013537133.1 1 MALIVQKFGGTSMGSIERIRLVAQRVLEEKEKGNQVVVVVSAMAGETDRLIELV------KSITPEPNE 63 579***************************************************......9******** PP TIGR00656 70 rerdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiiv 138 r +d +vs+GE++s+ lls l++lg+ a+al+g++agi Tdd f++A+i +++t er+l+ L+eg+iv lcl|NCBI__GCF_000185805.1:WP_013537133.1 64 RDMDFVVSTGEQVSAGLLSITLNHLGHPAVALSGWQAGIKTDDAFTKARIISIDT-ERILKHLKEGKIV 131 *******************************************************.************* PP TIGR00656 139 vvaGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEa 207 v++GF+G teeGeiTtLGRGGSD++A++laaal+Adr++iyTDV+Gvyt+DPr+v+ea+ki+ +syeE+ lcl|NCBI__GCF_000185805.1:WP_013537133.1 132 VITGFQGITEEGEITTLGRGGSDTSAVALAAALNADRCDIYTDVDGVYTADPRIVPEARKIPVLSYEEM 200 ********************************************************************* PP TIGR00656 208 lelAtlGakvlhpralelaveakvpilvrsskekeegTlitnkkens..slvkaialeknvarltvege 274 lelA+lGakvl+ r++e+a+++kvp++vrs+++++egTli ++ e+ +v++ia++kn ar+tv+ lcl|NCBI__GCF_000185805.1:WP_013537133.1 201 LELASLGAKVLQIRSVEFAMKYKVPLRVRSTFQPDEGTLIKEEDETMerVVVRGIAHNKNEARITVV-- 267 *****************************************9555444579****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340 + +k+gi+a++f aLae++i vd+i+q s t+is++vd++d+++a+k+ +++ ++++ +++ + lcl|NCBI__GCF_000185805.1:WP_013537133.1 268 RVPDKPGIAAKLFDALAEANIPVDMIVQNVSVdgyTDISFTVDKNDAQKAEKITQKVAQEIGAREVIRD 336 ****************************9987889********************************** PP TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 ++a+vsivg g++++ Gva+++f+ l++ +inilmis+se+kis ++dek +e avr lhe++ lcl|NCBI__GCF_000185805.1:WP_013537133.1 337 DKIAKVSIVGLGMRSHAGVAGKVFETLANYGINILMISTSEIKISCIIDEKFTELAVRVLHEAFG 401 **************************************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (406 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.76 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory